Health,
While Reb Mottel Zt”l was alive, he was undoubtedly in control of the ruchnius of the Yeshiva. Recently, and in my mind terribly, R’ Glustein was removed from his position (and then brought back in as Rosh Yeshiva Emiritus) and R’Zeffren was forced to retire.
This isn’t really relevant but the Yeshiva’s history before R’Glustein came back from Telz is more complicated. Merkaz Hatorah was started by R’Baron Zt”l and Yeshiva Gedola was started as a branch of Chofetz Chaim. They merged and became Yeshiva Gedola Merkaz Hatorah about 45 years ago under Rabbi Glustein’s leadership.